Align indole-3-glycerol-phosphate synthase; EC 4.1.1.48 (characterized, see rationale)
to candidate 8501006 DvMF_1743 Indole-3-glycerol-phosphate synthase (RefSeq)
Query= uniprot:B8DM44_DESVM (321 letters) >FitnessBrowser__Miya:8501006 Length = 321 Score = 634 bits (1635), Expect = 0.0 Identities = 321/321 (100%), Positives = 321/321 (100%) Query: 1 MLDRFRIAKQPELDRLRKLAEAGGMPAPLASGTGGGTPRPDFLRALRDRTGYPDAPVAVI 60 MLDRFRIAKQPELDRLRKLAEAGGMPAPLASGTGGGTPRPDFLRALRDRTGYPDAPVAVI Sbjct: 1 MLDRFRIAKQPELDRLRKLAEAGGMPAPLASGTGGGTPRPDFLRALRDRTGYPDAPVAVI 60 Query: 61 AEYKRASPSRGVIETGVSPEDAATAYATAGATAISVLTEEQYFGGDLTYLGRMAGVNPDV 120 AEYKRASPSRGVIETGVSPEDAATAYATAGATAISVLTEEQYFGGDLTYLGRMAGVNPDV Sbjct: 61 AEYKRASPSRGVIETGVSPEDAATAYATAGATAISVLTEEQYFGGDLTYLGRMAGVNPDV 120 Query: 121 PLLRKDFIMDSLQVAATAATPAAALLLIVRLTPDAHTLRDLREQAETHGMHAVVEIFDEA 180 PLLRKDFIMDSLQVAATAATPAAALLLIVRLTPDAHTLRDLREQAETHGMHAVVEIFDEA Sbjct: 121 PLLRKDFIMDSLQVAATAATPAAALLLIVRLTPDAHTLRDLREQAETHGMHAVVEIFDEA 180 Query: 181 DLALARESGARIIQVNNRDLETLAVDRTACLRLGPLRAPGEVWIAASGISENRHLAEAAA 240 DLALARESGARIIQVNNRDLETLAVDRTACLRLGPLRAPGEVWIAASGISENRHLAEAAA Sbjct: 181 DLALARESGARIIQVNNRDLETLAVDRTACLRLGPLRAPGEVWIAASGISENRHLAEAAA 240 Query: 241 AGYDAALVGTALMDGGDLKGSLMRLLGREGTPSFRPPASSGCAACSGHVRSEYAPCASGS 300 AGYDAALVGTALMDGGDLKGSLMRLLGREGTPSFRPPASSGCAACSGHVRSEYAPCASGS Sbjct: 241 AGYDAALVGTALMDGGDLKGSLMRLLGREGTPSFRPPASSGCAACSGHVRSEYAPCASGS 300 Query: 301 PSLPENENPVVPDCSETEGAQ 321 PSLPENENPVVPDCSETEGAQ Sbjct: 301 PSLPENENPVVPDCSETEGAQ 321 Lambda K H 0.316 0.133 0.386 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 540 Number of extensions: 13 Number of successful extensions: 1 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 321 Length of database: 321 Length adjustment: 28 Effective length of query: 293 Effective length of database: 293 Effective search space: 85849 Effective search space used: 85849 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory